Question: Hypothesis testing for isoform level TCGA RNA-seq expression data
gravatar for deepak18
13 months ago by
deepak1810 wrote:

I am working with isoform-level RNA-seq data from TCGA. After calculating isoform fraction (expression level of a particular isoform divided by the total expression of all the isoforms belonging to a gene) for all isoforms in cancer and tumor samples I wanted to check if the expression of a particular isoform is different between normal and cancer patient samples. To achieve this, I made a boxplot using this data but without any p-value because I did not perform any hypothesis test on this data. What kind of test can be performed on this kind of data?

PS: I am new to bioinformatics analysis, so any links to other online forums pertaining to the question would help.

tcga rna-seq next-gen R • 356 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 13 months ago by deepak1810

This comes down to differential transcript analysis. Use established tools such as, kallisto/sleuth or DEXSeq and then check if your isoform is among the DETs.

ADD REPLYlink written 13 months ago by ATpoint40k
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